Alignments for a candidate for asnB in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Azohydromonas australica DSM 1124

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_029001906.1 H537_RS0137180 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000430725.1:WP_029001906.1
          Length = 626

 Score =  336 bits (862), Expect = 2e-96
 Identities = 206/629 (32%), Positives = 336/629 (53%), Gaps = 30/629 (4%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+++       A    +++ M   + HRGPD  G+     VG G RRLSIID++ 
Sbjct: 1   MCGISGIYDFKGRPVDAG---VLQCMTHALAHRGPDGSGHLLRGPVGLGHRRLSIIDLDG 57

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPL+ EDE   I+FNGEIYN+IELREEL   G++F T SDTEV++  Y  + +   ++
Sbjct: 58  GAQPLANEDEKVHIVFNGEIYNFIELREELLKSGHSFKTRSDTEVIVHAYEQWGDACVNR 117

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMV-AQNDIEIDKE 179
             G+FAF IW++    L  ARD  GIKPLYY  ++ Q+ F SE K+L+        +D  
Sbjct: 118 FNGIFAFAIWDERQQRLLIARDHLGIKPLYYIEVDGQLLFGSEIKALLAHPACPRGVDTA 177

Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTE---EDK 236
           AL Q  +F++VP P+TL   ++K+ PG + T    G +  + Y+  N+ P   E   E+ 
Sbjct: 178 ALGQLFTFRYVPSPATLFDRIRKLPPGHRMTADAAG-LRIERYW--NWIPSHRESVNEEA 234

Query: 237 LVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAK-EFHPSLKTFSVGFE-QQG 294
           L +E    + D+V + +RSDVPVG FLS G+DS+ ++++ +      + TF++GFE  + 
Sbjct: 235 LAEEYGALVEDAVKLQLRSDVPVGLFLSSGVDSAALLAIMRSHLSGPINTFTIGFEGGER 294

Query: 295 FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKK 354
            +E + A+  A   G ++   ++SP +Y     + +W  ++P+ +  A    FV+  A +
Sbjct: 295 SNENEDARALARRFGADHSEMIVSPRDYEEYFTRYIWELEEPVGNETAAAFNFVSMIASR 354

Query: 355 HVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAV-MPEGMRGKSLLE 413
            V V L+G+GADE + GY+ +      + + ++P    + ++  A + +P   R    L+
Sbjct: 355 RVKVVLTGQGADEPWAGYHRHLGVKLSEYYRQLPGPFGRNVIRSAVMALPRNER----LK 410

Query: 414 RGCTPLQD-----RYIGNAKIFEESVKKQLL-KHYNPNLSY-----RDVTKTYFTESSSY 462
           RG   L +     R+      F   +++QL        +SY     R        +    
Sbjct: 411 RGVLALDEGDTLTRFAKIYSFFTPDMREQLFHSQVKGGMSYQSYETRQALAHLQHDVRQL 470

Query: 463 SDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGT 522
             +++M Y+D    +  D+L+  DKM+MA+S+E RVP+LD  + +    +P   K +  T
Sbjct: 471 DPVSQMLYMDTRANLPDDLLMVNDKMSMAHSIESRVPYLDVRLVEFVESLPTRYKLRFTT 530

Query: 523 TKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQTDAYIHKDY 580
            KYL +KA +  +P  V++RKK GF  PI  WL+  M   V+ ++   +S    Y + DY
Sbjct: 531 GKYLHKKALQRWLPRQVVHRKKKGFDNPIDIWLRERMKSRVQELLFSADSAIRQYFNVDY 590

Query: 581 VLQLLEDHCADKADNSRKIWTVLIFMIWH 609
           + QL+  H     +  R I+ ++ F +WH
Sbjct: 591 IRQLVRQHEEGSRNYMRHIYLLISFEMWH 619


Lambda     K      H
   0.319    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 952
Number of extensions: 55
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 626
Length adjustment: 38
Effective length of query: 594
Effective length of database: 588
Effective search space:   349272
Effective search space used:   349272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_029001906.1 H537_RS0137180 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.2025433.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-153  496.6   0.0   6.2e-153  496.4   0.0    1.0  1  NCBI__GCF_000430725.1:WP_029001906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_029001906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.4   0.0  6.2e-153  6.2e-153       1     517 []       2     555 ..       2     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 496.4 bits;  conditional E-value: 6.2e-153
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evv 72 
                                           Cgi gi d k   ++    ++ m+++lahRGPD++g+        ++lghrRL+iidl +gaQPl+ne+ +v 
  NCBI__GCF_000430725.1:WP_029001906.1   2 CGISGIYDFKGRPVD-AGVLQCMTHALAHRGPDGSGHLLR---GPVGLGHRRLSIIDLDGGAQPLANEDeKVH 70 
                                           *********998766.599*****************6555...9*************************999* PP

                             TIGR01536  73 ivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGi 145
                                           ivfnGEIYN+ eLreel + G++F+t+sDtEVi++aye+wg ++v+r++G FAfa+wde++++l++aRD+lGi
  NCBI__GCF_000430725.1:WP_029001906.1  71 IVFNGEIYNFIELREELLKSGHSFKTRSDTEVIVHAYEQWGDACVNRFNGIFAFAIWDERQQRLLIARDHLGI 143
                                           ************************************************************************* PP

                             TIGR01536 146 kPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekl 215
                                           kPLYy + +g+llf+SEiKalla+++ ++ +d +al +l+t+ +vp++ tlf ++++l+p++ +       ++
  NCBI__GCF_000430725.1:WP_029001906.1 144 KPLYYIEVDGQLLFGSEIKALLAHPACPRGVDTAALGQLFTFRYVPSPATLFDRIRKLPPGHRMtadAAGLRI 216
                                           ****************************************************************886666788 PP

                             TIGR01536 216 eeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigf 287
                                           e+yw+   ++  + +ee+l ee   l+edavk +l++dvpvg++lS+G+DS ++ ai++ ++ ++++tF+igf
  NCBI__GCF_000430725.1:WP_029001906.1 217 ERYWNWIPSHrESVNEEALAEEYGALVEDAVKLQLRSDVPVGLFLSSGVDSAALLAIMRSHLSGPINTFTIGF 289
                                           88**97554437889999******************************************************* PP

                             TIGR01536 288 edskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLs 360
                                           e+ +  +e++ ar++a+ +g +h e+++s+ ++ + + + i+ leep+ ++ ++   ++s  a+++ vkVvL+
  NCBI__GCF_000430725.1:WP_029001906.1 290 EGGERSNENEDARALARRFGADHSEMIVSPRDYEEYFTRYIWELEEPVGNETAAAFNFVSMIASRR-VKVVLT 361
                                           *****************************************************************9.****** PP

                             TIGR01536 361 GeGaDElfgGYeyfreakaeeale.........................lpeaselaekkl............ 396
                                           G+GaDE  +GY+++   k +e+ +                                                 
  NCBI__GCF_000430725.1:WP_029001906.1 362 GQGADEPWAGYHRHLGVKLSEYYRqlpgpfgrnvirsavmalprnerlkR----------Gvlaldegdtltr 424
                                           ***********************999999999988877766333333330..........1335555555666 PP

                             TIGR01536 397 ...........llqaklakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdllrak.Dr 457
                                                      + ++++++++  k  ++ ++ e+++   +l++++ +   ++++l+ d+   l+d+l++  D+
  NCBI__GCF_000430725.1:WP_029001906.1 425 fakiysfftpdMREQLFHSQV--KGGMSYQSYETRQALAHLQHDVRQLDPVSQMLYMDTRANLPDDLLMVnDK 495
                                           655566555533333333222..223334455566666777777777799*******99988888776655** PP

                             TIGR01536 458 vsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                           +smahs+E+RvP+lD +lve++ s+p+ +klr  + K+l ++a+++ lP+++++RkK++f
  NCBI__GCF_000430725.1:WP_029001906.1 496 MSMAHSIESRVPYLDVRLVEFVESLPTRYKLRFTTGKYLHKKALQRWLPRQVVHRKKKGF 555
                                           **********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (626 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.03s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.65
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis